workflows.dmri.camino.connectivity_mapping

create_connectivity_pipeline()

Link to code

Creates a pipeline that does the same connectivity processing as in the dMRI: Connectivity - Camino, CMTK, FreeSurfer example script. Given a subject id (and completed Freesurfer reconstruction) diffusion-weighted image, b-values, and b-vectors, the workflow will return the subject’s connectome as a Connectome File Format (CFF) file for use in Connectome Viewer (http://www.cmtk.org).

Example

>>> from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
>>> conmapper = create_connectivity_pipeline("nipype_conmap")
>>> conmapper.inputs.inputnode.subjects_dir = '.'
>>> conmapper.inputs.inputnode.subject_id = 'subj1'
>>> conmapper.inputs.inputnode.dwi = 'data.nii.gz'
>>> conmapper.inputs.inputnode.bvecs = 'bvecs'
>>> conmapper.inputs.inputnode.bvals = 'bvals'
>>> conmapper.run()                 

Inputs:

inputnode.subject_id
inputnode.subjects_dir
inputnode.dwi
inputnode.bvecs
inputnode.bvals
inputnode.resolution_network_file

Outputs:

outputnode.connectome
outputnode.cmatrix
outputnode.gpickled_network
outputnode.fa
outputnode.struct
outputnode.trace
outputnode.tracts
outputnode.tensors

Graph

digraph connectivity{

  label="connectivity";

  connectivity_inputnode[label="inputnode (utility)"];

  connectivity_outputnode[label="outputnode (utility)"];

  subgraph cluster_connectivity_mapping {

      label="mapping";

    connectivity_mapping_inputnode_within[label="inputnode_within (utility)"];

    connectivity_mapping_fssource[label="fssource (io)"];

    connectivity_mapping_mri_convert_Brain[label="mri_convert_Brain (freesurfer)"];

    connectivity_mapping_fssourceRH[label="fssourceRH (io)"];

    connectivity_mapping_mris_convertRH[label="mris_convertRH (freesurfer)"];

    connectivity_mapping_mris_convertRHlabels[label="mris_convertRHlabels (freesurfer)"];

    connectivity_mapping_mris_convertRHinflated[label="mris_convertRHinflated (freesurfer)"];

    connectivity_mapping_mris_convertRHsphere[label="mris_convertRHsphere (freesurfer)"];

    connectivity_mapping_mris_convertRHwhite[label="mris_convertRHwhite (freesurfer)"];

    connectivity_mapping_fsl2scheme[label="fsl2scheme (camino)"];

    connectivity_mapping_dtlutgen[label="dtlutgen (camino)"];

    connectivity_mapping_image2voxel[label="image2voxel (camino)"];

    connectivity_mapping_dtifit[label="dtifit (camino)"];

    connectivity_mapping_dteig[label="dteig (camino)"];

    connectivity_mapping_picopdfs[label="picopdfs (camino)"];

    connectivity_mapping_fa[label="fa (camino)"];

    connectivity_mapping_analyzeheader_fa[label="analyzeheader_fa (camino)"];

    connectivity_mapping_fa2nii[label="fa2nii (misc)"];

    connectivity_mapping_trace[label="trace (camino)"];

    connectivity_mapping_fssourceLH[label="fssourceLH (io)"];

    connectivity_mapping_mris_convertLHlabels[label="mris_convertLHlabels (freesurfer)"];

    connectivity_mapping_GiftiLabels[label="GiftiLabels (utility)"];

    connectivity_mapping_mris_convertLHinflated[label="mris_convertLHinflated (freesurfer)"];

    connectivity_mapping_mris_convertLHsphere[label="mris_convertLHsphere (freesurfer)"];

    connectivity_mapping_mris_convertLHwhite[label="mris_convertLHwhite (freesurfer)"];

    connectivity_mapping_mris_convertLH[label="mris_convertLH (freesurfer)"];

    connectivity_mapping_GiftiSurfaces[label="GiftiSurfaces (utility)"];

    connectivity_mapping_mri_convert_AparcAseg[label="mri_convert_AparcAseg (freesurfer)"];

    connectivity_mapping_ROIGen_structspace[label="ROIGen_structspace (cmtk)"];

    connectivity_mapping_CreateNodes[label="CreateNodes (cmtk)"];

    connectivity_mapping_bet_b0[label="bet_b0 (fsl)"];

    connectivity_mapping_track[label="track (camino)"];

    connectivity_mapping_camino2trackvis[label="camino2trackvis (camino2trackvis)"];

    connectivity_mapping_trk2camino[label="trk2camino (camino2trackvis)"];

    connectivity_mapping_vtkstreamlines[label="vtkstreamlines (camino)"];

    connectivity_mapping_coregister[label="coregister (fsl)"];

    connectivity_mapping_convertxfm[label="convertxfm (fsl)"];

    connectivity_mapping_inverse[label="inverse (fsl)"];

    connectivity_mapping_inverse_AparcAseg[label="inverse_AparcAseg (fsl)"];

    connectivity_mapping_ROIGen[label="ROIGen (cmtk)"];

    connectivity_mapping_CreateMatrix[label="CreateMatrix (cmtk)"];

    connectivity_mapping_FiberDataArrays[label="FiberDataArrays (utility)"];

    connectivity_mapping_NiftiVolumes[label="NiftiVolumes (utility)"];

    connectivity_mapping_CFFConverter[label="CFFConverter (cmtk)"];

    connectivity_mapping_analyzeheader_trace[label="analyzeheader_trace (camino)"];

    connectivity_mapping_trace2nii[label="trace2nii (misc)"];

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceLH;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceLH;

    connectivity_mapping_inputnode_within -> connectivity_mapping_trace2nii;

    connectivity_mapping_inputnode_within -> connectivity_mapping_NiftiVolumes;

    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_fa;

    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_fa;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssource;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssource;

    connectivity_mapping_inputnode_within -> connectivity_mapping_camino2trackvis;

    connectivity_mapping_inputnode_within -> connectivity_mapping_camino2trackvis;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceRH;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceRH;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fa2nii;

    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_trace;

    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_trace;

    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateMatrix;

    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateMatrix;

    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateNodes;

    connectivity_mapping_inputnode_within -> connectivity_mapping_bet_b0;

    connectivity_mapping_inputnode_within -> connectivity_mapping_bet_b0;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fsl2scheme;

    connectivity_mapping_inputnode_within -> connectivity_mapping_fsl2scheme;

    connectivity_mapping_inputnode_within -> connectivity_mapping_image2voxel;

    connectivity_mapping_inputnode_within -> connectivity_mapping_CFFConverter;

    connectivity_mapping_fssource -> connectivity_mapping_mri_convert_Brain;

    connectivity_mapping_fssource -> connectivity_mapping_mri_convert_AparcAseg;

    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_inverse;

    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_coregister;

    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_NiftiVolumes;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRH;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHlabels;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHlabels;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHinflated;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHsphere;

    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHwhite;

    connectivity_mapping_mris_convertRH -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertRHlabels -> connectivity_mapping_GiftiLabels;

    connectivity_mapping_mris_convertRHinflated -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertRHsphere -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertRHwhite -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_fsl2scheme -> connectivity_mapping_dtifit;

    connectivity_mapping_fsl2scheme -> connectivity_mapping_dtlutgen;

    connectivity_mapping_dtlutgen -> connectivity_mapping_picopdfs;

    connectivity_mapping_image2voxel -> connectivity_mapping_dtifit;

    connectivity_mapping_dtifit -> connectivity_mapping_dteig;

    connectivity_mapping_dtifit -> connectivity_mapping_picopdfs;

    connectivity_mapping_dtifit -> connectivity_mapping_fa;

    connectivity_mapping_dtifit -> connectivity_mapping_trace;

    connectivity_mapping_picopdfs -> connectivity_mapping_track;

    connectivity_mapping_fa -> connectivity_mapping_analyzeheader_fa;

    connectivity_mapping_fa -> connectivity_mapping_fa2nii;

    connectivity_mapping_analyzeheader_fa -> connectivity_mapping_fa2nii;

    connectivity_mapping_trace -> connectivity_mapping_analyzeheader_trace;

    connectivity_mapping_trace -> connectivity_mapping_trace2nii;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLH;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHlabels;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHlabels;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHinflated;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHsphere;

    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHwhite;

    connectivity_mapping_mris_convertLHlabels -> connectivity_mapping_GiftiLabels;

    connectivity_mapping_GiftiLabels -> connectivity_mapping_CFFConverter;

    connectivity_mapping_mris_convertLHinflated -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertLHsphere -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertLHwhite -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_mris_convertLH -> connectivity_mapping_GiftiSurfaces;

    connectivity_mapping_GiftiSurfaces -> connectivity_mapping_CFFConverter;

    connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_inverse_AparcAseg;

    connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_ROIGen_structspace;

    connectivity_mapping_ROIGen_structspace -> connectivity_mapping_CreateNodes;

    connectivity_mapping_CreateNodes -> connectivity_mapping_CreateMatrix;

    connectivity_mapping_bet_b0 -> connectivity_mapping_inverse;

    connectivity_mapping_bet_b0 -> connectivity_mapping_inverse_AparcAseg;

    connectivity_mapping_bet_b0 -> connectivity_mapping_coregister;

    connectivity_mapping_bet_b0 -> connectivity_mapping_track;

    connectivity_mapping_track -> connectivity_mapping_camino2trackvis;

    connectivity_mapping_track -> connectivity_mapping_vtkstreamlines;

    connectivity_mapping_camino2trackvis -> connectivity_mapping_trk2camino;

    connectivity_mapping_camino2trackvis -> connectivity_mapping_CFFConverter;

    connectivity_mapping_camino2trackvis -> connectivity_mapping_CreateMatrix;

    connectivity_mapping_coregister -> connectivity_mapping_convertxfm;

    connectivity_mapping_convertxfm -> connectivity_mapping_inverse;

    connectivity_mapping_convertxfm -> connectivity_mapping_inverse_AparcAseg;

    connectivity_mapping_inverse_AparcAseg -> connectivity_mapping_ROIGen;

    connectivity_mapping_ROIGen -> connectivity_mapping_CreateMatrix;

    connectivity_mapping_ROIGen -> connectivity_mapping_NiftiVolumes;

    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

    connectivity_mapping_CreateMatrix -> connectivity_mapping_CFFConverter;

    connectivity_mapping_FiberDataArrays -> connectivity_mapping_CFFConverter;

    connectivity_mapping_NiftiVolumes -> connectivity_mapping_CFFConverter;

    connectivity_mapping_analyzeheader_trace -> connectivity_mapping_trace2nii;

  }

  connectivity_mapping_camino2trackvis -> connectivity_outputnode;

  connectivity_mapping_CFFConverter -> connectivity_outputnode;

  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

  connectivity_mapping_fa2nii -> connectivity_outputnode;

  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

  connectivity_mapping_ROIGen -> connectivity_outputnode;

  connectivity_mapping_mri_convert_Brain -> connectivity_outputnode;

  connectivity_mapping_trace2nii -> connectivity_outputnode;

  connectivity_mapping_dtifit -> connectivity_outputnode;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

  connectivity_inputnode -> connectivity_mapping_inputnode_within;

}